The present invention relates to devices for screening attributes of chemical compounds, and in particular, to a method and apparatus for flexibly producing arrays of different chemically active substances for large scale chemical screening and assaying.
The analysis of chemical substances (e.g., nucleotide sequences) may be facilitated by the preparation of an array having many different chemical compounds (sampling compounds) placed at known sites. Each sampling compound selectively bonds with a different substance that may be part of the material to be analyzed. The sampling compounds are arranged in a regular pattern of array elements over the plane of the array.
In the field of genetic research, the sampling compounds may be different oligonucleotides at least one of which is expected to hybridize with portions of a genetic material to be tested. Fluorescent or radioactive markers bonded to the genetic material to be tested, or other well-known techniques, may be used to determine the location of the hybridizations, and from these locations (and a map of known locations of the sample oligonucleotides in the planar array), information about the make-up or other attributes of the genetic material may be determined.
A number of different methods have been used to create such arrays of different sampling compounds. In one sequential method, different sampling compounds are synthesized and placed in different wells of a microtiter place. The sampling compounds are then transferred from a microtiter plate to one or more array substrates by a robotically controlled dipping stick immersed first in a sampling compound then touched to different elements of the array where that sampling compound is to be located. In the case where the sampling compounds are oligonucleotides, the components are nucleic acids generated by using PCR and suitable templates.
A variation on this system, particularly useful in the generation of oligonucleotides, employs an ink jet-type process similar to that used in standard commercial printers to build up the sampling compounds, one component at a time, through layers laid down on particular elements of the array in a spatially controlled manner. For oligonucleotides, the process cycles through each of the four nucleic acids so that arbitrary oligonucleotides may be formed at the different array elements.
An alternative approach that processes many elements in parallel creates a series of masks, for example, using photolithographic techniques, where the masks have openings over specified array elements where a component is to be deposited. After each mask is in place, the desired component is washed over the mask and attaches only to those array elements corresponding to an open mask position. The mask is then removed and a new mask laid in place and this process repeated with a different component, for example, a different nucleic acid.
The laborious process of generating, applying and removing masks may be eliminated through the use photo-activation techniques in which the constituent components to be applied to array elements are suffused at the surface of the array and selective array elements irradiated with light to bond the components only at the illuminated elements. Mirror systems using micro-machined mirrors to direct intense light selectively to different portions in the array provide simultaneous processing of many array elements.
While this last technique eliminates the need for mask generation, constraints in maximum light flux that can be controlled, limit the speed at which arrays may be formed. Generally, mask techniques will be used when large numbers of a given type of array must be produced and sequential or mask-less photo activation techniques will be used for limited productions of different types of arrays.
A tradeoff between the speed of manufacturing the arrays and flexibility in manufacturing arrays of different types is provided by forming the different sampling compounds of an array on small beads. Those beads having a given sampling compound may be manufactured using parallel processing techniques. Later, beads with different sampling compounds are mechanically assembled into arrays using robotic manipulation or the like.
It is in this latter stage of manipulating the beads into usable arrays, that the shortcoming of using beads becomes most pronounced, and that causes, as a practical matter, the use of beads in manufacturing planar arrays, to be limited.